python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS135_hiPSC_WTC-11_NTC_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS135_hiPSC_WTC-11_NTC_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.counts 
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS136_hiPSC_WTC-11_NTC_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS136_hiPSC_WTC-11_NTC_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.counts 
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS137_hiPSC_WTC-11_NTC_CRISPRi_3.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS137_hiPSC_WTC-11_NTC_CRISPRi_3.2x50mers.hs1-T2T-CHM13v2.0.a.counts 
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS138_hiPSC_WTC-11_TASOR2_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS138_hiPSC_WTC-11_TASOR2_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.counts 
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS139_hiPSC_WTC-11_TASOR2_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS139_hiPSC_WTC-11_TASOR2_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.counts 
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS140_hiPSC_WTC-11_TASOR2_CRISPRi_3.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS140_hiPSC_WTC-11_TASOR2_CRISPRi_3.2x50mers.hs1-T2T-CHM13v2.0.a.counts 
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS141_hiPSC_WTC-11_TASOR_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS141_hiPSC_WTC-11_TASOR_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.counts 
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS142_hiPSC_WTC-11_TASOR_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS142_hiPSC_WTC-11_TASOR_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.counts 
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS143_hiPSC_WTC-11_MPP8_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS143_hiPSC_WTC-11_MPP8_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.counts 
python ~/code/bedRawReadCountsBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS144_hiPSC_WTC-11_MPP8_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam hs1.repeatMasker.MS144_hiPSC_WTC-11_MPP8_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.counts 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS135_hiPSC_WTC-11_NTC_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.chrom.sizes hs1.repeatMasker.MS135_hiPSC_WTC-11_NTC_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM 
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS136_hiPSC_WTC-11_NTC_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.chrom.sizes hs1.repeatMasker.MS136_hiPSC_WTC-11_NTC_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS137_hiPSC_WTC-11_NTC_CRISPRi_3.2x50mers.hs1-T2T-CHM13v2.0.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.chrom.sizes hs1.repeatMasker.MS137_hiPSC_WTC-11_NTC_CRISPRi_3.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS138_hiPSC_WTC-11_TASOR2_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.chrom.sizes hs1.repeatMasker.MS138_hiPSC_WTC-11_TASOR2_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS139_hiPSC_WTC-11_TASOR2_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.chrom.sizes hs1.repeatMasker.MS139_hiPSC_WTC-11_TASOR2_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS140_hiPSC_WTC-11_TASOR2_CRISPRi_3.2x50mers.hs1-T2T-CHM13v2.0.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.chrom.sizes hs1.repeatMasker.MS140_hiPSC_WTC-11_TASOR2_CRISPRi_3.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS141_hiPSC_WTC-11_TASOR_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.chrom.sizes hs1.repeatMasker.MS141_hiPSC_WTC-11_TASOR_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS142_hiPSC_WTC-11_TASOR_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.chrom.sizes hs1.repeatMasker.MS142_hiPSC_WTC-11_TASOR_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS143_hiPSC_WTC-11_MPP8_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.chrom.sizes hs1.repeatMasker.MS143_hiPSC_WTC-11_MPP8_CRISPRi_1.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM
python ~/code/bedRPKMfromBAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.repeatMasker.out.tab.gz 4 MS144_hiPSC_WTC-11_MPP8_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/hs1-T2T-CHM13v2.0/hs1.chrom.sizes hs1.repeatMasker.MS144_hiPSC_WTC-11_MPP8_CRISPRi_2.2x50mers.hs1-T2T-CHM13v2.0.a.RPKM